Alternatives and similar repositories for openproblems

Users that are interested in openproblems are comparing it to the libraries listed below

• theislab / scib
  Benchmarking analysis of data integration tools
  ☆373Updated 6 months ago
• theislab / scarches
  Reference mapping for single-cell genomics
  ☆375Updated 2 weeks ago
• morris-lab / CellOracle
  This is the alpha version of the CellOracle package
  ☆372Updated 7 months ago
• scverse / pertpy
  Single-cell perturbation analysis
  ☆194Updated this week
• theislab / cellrank
  CellRank: dynamics from multi-view single-cell data
  ☆393Updated 4 months ago
• theislab / scgen
  Single cell perturbation prediction
  ☆312Updated 8 months ago
• aristoteleo / dynamo-release
  Inclusive model of expression dynamics with conventional or metabolic labeling based scRNA-seq / multiomics, vector field reconstruction …
  ☆465Updated last month
• scverse / scanpy-tutorials
  Scanpy Tutorials.
  ☆219Updated last week
• Genentech / scimilarity
  A unifying representation of single cell expression profiles that quantifies similarity between expression states and generalizes to repr…
  ☆210Updated last month
• BayraktarLab / cell2location
  Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)
  ☆372Updated last month
• gao-lab / GLUE
  Graph-linked unified embedding for single-cell multi-omics data integration
  ☆419Updated last month
• Teichlab / celltypist
  A tool for semi-automatic cell type classification
  ☆395Updated this week
• scverse / decoupler
  Python package to perform enrichment analysis from omics data.
  ☆215Updated this week
• scverse / muon
  muon is a multimodal omics Python framework
  ☆240Updated 5 months ago
• theislab / scvelo
  RNA Velocity generalized through dynamical modeling
  ☆456Updated 5 months ago
• agitter / single-cell-pseudotime
  An overview of algorithms for estimating pseudotime in single-cell RNA-seq data
  ☆426Updated last week
• theislab / sc-pert
  Models and datasets for perturbational single-cell omics
  ☆155Updated 2 years ago
• broadinstitute / Tangram
  Spatial alignment of single cell transcriptomic data.
  ☆313Updated last month
• crazyhottommy / awesome_spatial_omics
  tools and notes for spatial omics
  ☆311Updated 5 months ago
• saezlab / liana-py
  LIANA+: an all-in-one framework for cell-cell communication
  ☆224Updated 3 weeks ago
• dylkot / cNMF
  Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data
  ☆355Updated 5 months ago
• slowkow / harmonypy
  🎼 Integrate multiple high-dimensional datasets with fuzzy k-means and locally linear adjustments.
  ☆222Updated last year
• KrishnaswamyLab / MAGIC
  MAGIC (Markov Affinity-based Graph Imputation of Cells), is a method for imputing missing values restoring structure of large biological …
  ☆367Updated 10 months ago
• scverse / scirpy
  A scanpy extension to analyse single-cell TCR and BCR data.
  ☆236Updated this week
• theislab / diffxpy
  Differential expression analysis for single-cell RNA-seq data.
  ☆200Updated 5 months ago
• brianhie / scanorama
  Panoramic stitching of single cell data
  ☆286Updated 3 weeks ago
• theislab / moscot
  Multi-omic single-cell optimal transport tools
  ☆167Updated last week
• dynverse / dynbenchmark
  Comparison of methods for trajectory inference on single-cell data 🥇
  ☆213Updated last year
• BiomedicalMachineLearning / stLearn
  A novel machine learning pipeline to analyse spatial transcriptomics data
  ☆226Updated last month
• theislab / single-cell-transformer-papers
  ☆323Updated 2 months ago